Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009428.1 Hibiscus syriacus cultivar Beakdansim tig00113406_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 97226
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:10538 original size:13 final size:13
Alignment explanation
Indices: 10516--10545 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10506 ACTAAACACC
10516 TTTC-ACATACCT
1 TTTCAACATACCT
10528 TTTCAACATACCT
1 TTTCAACATACCT
10541 TTTCA
1 TTTCA
10546 TCTTTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:28459 original size:17 final size:16
Alignment explanation
Indices: 28390--28461 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
28380 ATTCATGCAT
28390 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
28407 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* *
28425 GTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
28442 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
28459 CTA
1 CTA
28462 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.02
17 28 0.61
18 17 0.37
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:30323 original size:2 final size:2
Alignment explanation
Indices: 30312--30405 Score: 181
Period size: 2 Copynumber: 47.5 Consensus size: 2
30302 TAACTATAGG
30312 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30395 TA TA TA TA TA T
1 TA TA TA TA TA T
30406 GAAAATAACT
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 90 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33276 original size:5 final size:5
Alignment explanation
Indices: 33266--33321 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
33256 CTCTTTTGAA
* *
33266 TTTCT TTTCT TTTCT TTT-T TTTGATT TTTCT TTTCT TTTCT CTTTTT
1 TTTCT TTTCT TTTCT TTTCT TTT--CT TTTCT TTTCT TTTCT -TTTCT
33313 CTTTCT TTT
1 -TTTCT TTT
33322 TGTACTCCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.09
5 27 0.61
6 9 0.20
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:33311 original size:17 final size:18
Alignment explanation
Indices: 33273--33321 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
33263 GAATTTCTTT
33273 TCTTTTCTTTT-TTTTGA
1 TCTTTTCTTTTCTTTTGA
*
33290 T-TTTTCTTTTCTTTT-C
1 TCTTTTCTTTTCTTTTGA
33306 TCTTTT-TCTTTCTTTT
1 TCTTTTCT-TTTCTTTT
33322 TGTACTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTGA
Found at i:33681 original size:20 final size:21
Alignment explanation
Indices: 33644--33682 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
33634 GATGGTCTTG
*
33644 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
33665 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
33683 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:35595 original size:11 final size:11
Alignment explanation
Indices: 35579--35606 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
35569 ATTTTTTTTC
35579 AAAAAAAACAA
1 AAAAAAAACAA
35590 AAAAAAAACAA
1 AAAAAAAACAA
35601 AAAAAA
1 AAAAAA
35607 GGCAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:39918 original size:15 final size:15
Alignment explanation
Indices: 39886--39924 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
39876 CTTTATTATC
39886 TTATTTCATCTTCCGT
1 TTATTT-ATCTTCCGT
**
39902 TTATTTATCTTTTGT
1 TTATTTATCTTCCGT
39917 TTATTTAT
1 TTATTTAT
39925 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (15 bp):
TTATTTATCTTCCGT
Found at i:43812 original size:29 final size:29
Alignment explanation
Indices: 43780--43837 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
43770 TTGTTTAATC
43780 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
*
43809 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
43838 CAGTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.05, G:0.16, T:0.62
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:51369 original size:11 final size:11
Alignment explanation
Indices: 51355--51410 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
51345 TCTTTTTGAA
51355 TTCTTTTTCTT
1 TTCTTTTTCTT
51366 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
51379 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
51392 TGTCTTTTTC-T
1 T-TCTTTTTCTT
51403 TTCTTTTT
1 TTCTTTTT
51411 ACACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:51379 original size:19 final size:18
Alignment explanation
Indices: 51355--51410 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
51345 TCTTTTTGAA
51355 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
51373 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
51392 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
51410 T
1 T
51411 ACACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:56861 original size:34 final size:34
Alignment explanation
Indices: 56818--56887 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
56808 GTTGCATATG
56818 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
1 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
56852 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
1 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
56886 TT
1 TT
56888 CAGACTAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
Found at i:75664 original size:40 final size:40
Alignment explanation
Indices: 75620--75698 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 40
75610 TGATCTACCC
75620 TCGTTTGCCTTTTACGCGCT-TTCTCTCTTGTGGGTCCCTT
1 TCGTTTGCCTTTTAC-CGCTATTCTCTCTTGTGGGTCCCTT
75660 TCGTTTGCCTTTTACCGCTCGATTCTCTCTTGTGGGTCC
1 TCGTTTGCCTTTTACCGCT--ATTCTCTCTTGTGGGTCC
75699 TTTTTAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
39 4 0.11
40 15 0.42
42 17 0.47
ACGTcount: A:0.04, C:0.30, G:0.20, T:0.46
Consensus pattern (40 bp):
TCGTTTGCCTTTTACCGCTATTCTCTCTTGTGGGTCCCTT
Done.